MolNFT v1 · #169311 · protein

Crystal structure of tnfalpha with isoquinoline compound 2

6X81 · Tumor necrosis factor: “Crystal structure of tnfalpha with isoquinoline compound 2”. X-ray diffraction, 1 ligand (UTJ), 13 pockets (best druggability 0.85). MolNFT v1 #169311 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6X81
Type: protein
Length: 852 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor
UniProt: P01375
Ligands: UTJ
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 1% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor	protein	145	2% helix, 52% strand	P01375
B	Tumor necrosis factor	protein	146	0% helix, 50% strand	P01375
C	Tumor necrosis factor	protein	144	0% helix, 52% strand	P01375
D	Tumor necrosis factor	protein	141	4% helix, 53% strand	P01375
E	Tumor necrosis factor	protein	132	2% helix, 52% strand	P01375
F	Tumor necrosis factor	protein	144	0% helix, 51% strand	P01375

Ligands and binding sites

UTJ · [4-(isoquinolin-8-yl)phenyl]acetonitrile · ligand · 4 copies · chains A, B, C, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	406	0.85	0.93	52	UTJ
2	1002	0.83	0.84	80	empty
3	382	0.82	0.91	45	UTJ
4	423	0.76	0.85	46	empty
5	751	0.74	0.79	70	empty

Interfaces

10 interfaces between chains.

B–C · 1193 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1065 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 1003 Å² buried · 7 hydrogen bonds · protein-protein
D–F · 897 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 656 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6X81 · Crystal Structure of TNFalpha with isoquinoline compound 2 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P01375
Elsewhere: RCSB PDB 6X81 · PDBe 6X81 · UniProt P01375

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